MetNetComp Database [1] / Minimal gene deletions Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : udpgalfur_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (85 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 66
  Gene deletion: b2242 b3553 b1478 b3399 b1241 b0351 b4069 b2502 b2744 b1278 b3708 b3614 b0910 b2297 b2458 b2779 b2781 b1612 b1611 b4122 b1759 b3962 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1033 b0596 b4374 b0675 b2361 b2291 b1415 b1014 b2799 b3945 b4388 b1907 b4138 b4123 b0621 b0112 b2868 b0114 b0529 b1539 b2492 b0904 b1533 b3825 b3028 b1380 b3918 b0508 b1473 b0494 b1511 b4266 b2842 b1206 b0404 b1090   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.255753 (mmol/gDw/h)
  Minimum Production Rate : 0.679546 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.484318
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.666220
  EX_pi_e : 1.605794
  EX_so4_e : 0.064404
  EX_k_e : 0.049921
  EX_fe2_e : 0.004108
  EX_mg2_e : 0.002219
  EX_ca2_e : 0.001331
  EX_cl_e : 0.001331
  EX_cu2_e : 0.000181
  EX_mn2_e : 0.000177
  EX_zn2_e : 0.000087
  EX_ni2_e : 0.000083

Product: (mmol/gDw/h)
  EX_h2o_e : 48.344847
  EX_co2_e : 29.091204
  EX_h_e : 8.684694
  EX_ac_e : 1.294204
  EX_succ_e : 1.247671
  Auxiliary production reaction : 0.679546
  EX_ade_e : 0.490487
  EX_ura_e : 0.046292
  EX_dxylnt_e : 0.000171
  DM_mththf_c : 0.000115
  DM_5drib_c : 0.000058
  DM_4crsol_c : 0.000057

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

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Last updated: 21-Sep-2023
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